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Forum: RNA Sequencing 08-05-2013, 11:54 PM
Replies: 1
Views: 2,577
Posted By fubar
A source download of Galaxy doesn't include many...

A source download of Galaxy doesn't include many third party dependencies, genomes or indices and requires a fair bit of additional installation and tweaking to get everything working - eg see...
Forum: Bioinformatics 10-09-2012, 08:52 PM
Replies: 4
Views: 12,226
Posted By fubar
The answer depends on exactly what you mean by...

The answer depends on exactly what you mean by "into Galaxy" :)
1. No, not on the public Galaxy instances run by the Galaxy Team.
2. Yes, if you have your own Galaxy. There's at least one suitable...
Forum: Bioinformatics 10-09-2012, 04:18 PM
Replies: 6
Views: 1,695
Posted By fubar
Yes is the answer to your question as quoted...

Yes is the answer to your question as quoted above.
You might have meant to ask how: I usually filter one or more fastq files using the fastx toolkit wrappers in our local Galaxy which fires off...
Forum: RNA Sequencing 10-07-2012, 03:00 AM
Replies: 5
Views: 1,519
Posted By fubar
It's hard to figure out where things are, but...

It's hard to figure out where things are, but there is at least some hapmap CEU sample RNAseq (eg) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25030 in GEO?
Forum: RNA Sequencing 10-03-2012, 06:05 AM
Replies: 2
Views: 1,841
Posted By fubar
Hi Sachitad, If you can't find a wrapper in the...

Hi Sachitad,
If you can't find a wrapper in the main Galaxy toolshed, then maybe ask on the Galaxy user list - please see some suggestions for getting a good result at ...
Forum: RNA Sequencing 10-06-2011, 12:20 AM
Replies: 7
Views: 11,343
Posted By fubar
I'm glad it worked for you but perplexed since...

I'm glad it worked for you but perplexed since the documentation at http://bio-bwa.sourceforge.net/bwa.shtml seems to make it clear that bwa accepts (and indexes) reference genomes as fasta but...
Forum: RNA Sequencing 09-30-2011, 08:01 PM
Replies: 7
Views: 11,343
Posted By fubar
I'm sure you have already read the documentation...

I'm sure you have already read the documentation for BWA, since it would be inconsiderate to waste bandwidth with this question otherwise? Since you seem to have missed it, no - fasta does not...
Forum: Core Facilities 11-10-2010, 08:35 AM
Replies: 8
Views: 5,998
Posted By fubar
(I'm a Galaxy developer so my views are probably...

(I'm a Galaxy developer so my views are probably biased)

Short answer: Security is a complex issue and there are no simple short answers other than from marketing droids...

Longer answer: There...
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